PINE-SPARKY Tutorial and Reference Manual

Last Updated: Dec 07, 2010

I. Introduction

 1. What is “PINE”?

 2. What is “SPARKY” and its extensions?

 3. What is the goal of this project?

 4. System Requirements

 5. Installation steps (Download)

II. PINE2SPARKY

 1. How can “PINE2SPARKY” converter imply many probabilities from PINE?

 2. User Interface

 3. Usage

III. SPARKY extensions

 1. PINE Assigner

 1) What is “PINE Assigner”?

 2) User Interface

 3) Usage

 2. PINE Graph Assigner

 1) What is “PINE Graph Assigner”?

 2) User Interface

 3) Usage

 3. Assign the best by PINE

 1) What is “Assign the best by PINE”?

 2) Usage

IV. Test

 1. Ubiquitin

 1) PINE results

 2) PINE-SPARKY results

V. Contact information

nputmanbuehl@wisc.edu
NMRFAM(National Magnetic Resonance Facilities at Madison)
Department of Biochemistry
University of Wisconsin-Madison

VI. Citation

Bioinformatics. 2009 Aug 15;25(16):2085-7. Epub 2009 Jun 3.
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy.

Lee W, Westler WM, Bahrami A, Eghbalnia HR, Markley JL.

National Magnetic Resonance Facility at Madison and Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA. whlee@nmrfam.wisc.edu